Ancient DNA is typically highly degraded with appreciable cytosine deamination, and contamination with present-day DNA often complicates the identification of endogenous molecules. Together, these ...factors impede accurate assembly of the endogenous ancient mitochondrial genome. We present schmutzi, an iterative approach to jointly estimate present-day human contamination in ancient human DNA datasets and reconstruct the endogenous mitochondrial genome. By using sequence deamination patterns and fragment length distributions, schmutzi accurately reconstructs the endogenous mitochondrial genome sequence even when contamination exceeds 50 %. Given sufficient coverage, schmutzi also produces reliable estimates of contamination across a range of contamination rates.
https://bioinf.eva.mpg.de/schmutzi/ license:GPLv3.
Neanderthals and Denisovans are extinct groups of hominins that separated from each other more than 390,000 years ago
. Here we present the genome of 'Denisova 11', a bone fragment from Denisova Cave ...(Russia)
and show that it comes from an individual who had a Neanderthal mother and a Denisovan father. The father, whose genome bears traces of Neanderthal ancestry, came from a population related to a later Denisovan found in the cave
. The mother came from a population more closely related to Neanderthals who lived later in Europe
than to an earlier Neanderthal found in Denisova Cave
, suggesting that migrations of Neanderthals between eastern and western Eurasia occurred sometime after 120,000 years ago. The finding of a first-generation Neanderthal-Denisovan offspring among the small number of archaic specimens sequenced to date suggests that mixing between Late Pleistocene hominin groups was common when they met.
A high-coverage Neandertal genome from Chagyrskaya Cave Mafessoni, Fabrizio; Grote, Steffi; de Filippo, Cesare ...
Proceedings of the National Academy of Sciences - PNAS,
06/2020, Letnik:
117, Številka:
26
Journal Article
Recenzirano
Odprti dostop
We sequenced the genome of a Neandertal from Chagyrskaya Cave in the Altai Mountains, Russia, to 27-fold genomic coverage. We show that this Neandertal was a female and that she was more related to ...Neandertals in western Eurasia Prüfer et al., Science 358, 655–658 (2017); Hajdinjak et al., Nature 555, 652–656 (2018) than to Neandertals who lived earlier in Denisova Cave Prüfer et al., Nature 505, 43–49 (2014), which is located about 100 km away. About 12.9% of the Chagyrskaya genome is spanned by homozygous regions that are between 2.5 and 10 centiMorgans (cM) long. This is consistent with the fact that Siberian Neandertals lived in relatively isolated populations of less than 60 individuals. In contrast, a Neandertal from Europe, a Denisovan from the Altai Mountains, and ancient modern humans seem to have lived in populations of larger sizes. The availability of three Neandertal genomes of high quality allows a view of genetic features that were unique to Neandertals and that are likely to have been at high frequency among them. We find that genes highly expressed in the striatum in the basal ganglia of the brain carry more aminoacid- changing substitutions than genes expressed elsewhere in the brain, suggesting that the striatum may have evolved unique functions in Neandertals.
A late Middle Pleistocene mandible from Baishiya Karst Cave (BKC) on the Tibetan Plateau has been inferred to be from a Denisovan, an Asian hominin related to Neanderthals, on the basis of an amino ...acid substitution in its collagen. Here we describe the stratigraphy, chronology, and mitochondrial DNA extracted from the sediments in BKC. We recover Denisovan mitochondrial DNA from sediments deposited ~100 thousand and ~60 thousand years ago (ka) and possibly as recently as ~45 ka. The long-term occupation of BKC by Denisovans suggests that they may have adapted to life at high altitudes and may have contributed such adaptations to modern humans on the Tibetan Plateau.
The intervertebral disc's (IVD) annulus fibrosus (AF) retains the hydrostatic pressure of the nucleus pulposus (NP), controls the range of motion, and maintains the integrity of the motion segment. ...The microstructure of the AF is not yet fully understood and quantitative characterization is lacking, leaving a caveat in modern medicine's ability to prevent and treat disc failure (e.g., disc herniation). In this study, we show a reconstruction of the 3D microstructure of the fibers that constitute the AF via MRI diffusion tensor imaging (DTI) followed by fiber tracking. A quantitative analysis presents an anisotropic structure with significant architectural differences among the annuli along the width of the fibrous belt. These findings indicate that the outer annuli's construction reinforces the IVD while providing a sufficient degree of motion. Our findings also suggest an increased role of the outer annuli in IVD nourishment.
Bones and teeth are important sources of Pleistocene hominin DNA, but are rarely recovered at archaeological sites. Mitochondrial DNA (mtDNA) has been retrieved from cave sediments but provides ...limited value for studying population relationships. We therefore developed methods for the enrichment and analysis of nuclear DNA from sediments and applied them to cave deposits in western Europe and southern Siberia dated to between 200,000 and 50,000 years ago. We detected a population replacement in northern Spain about 100,000 years ago, which was accompanied by a turnover of mtDNA. We also identified two radiation events in Neanderthal history during the early part of the Late Pleistocene. Our work lays the ground for studying the population history of ancient hominins from trace amounts of nuclear DNA in sediments.
Denisova Cave in southern Siberia is the type locality of the Denisovans, an archaic hominin group who were related to Neanderthals.sup.1-4. The dozen hominin remains recovered from the deposits also ...include Neanderthals.sup.5,6 and the child of a Neanderthal and a Denisovan.sup.7, which suggests that Denisova Cave was a contact zone between these archaic hominins. However, uncertainties persist about the order in which these groups appeared at the site, the timing and environmental context of hominin occupation, and the association of particular hominin groups with archaeological assemblages.sup.5,8-11. Here we report the analysis of DNA from 728 sediment samples that were collected in a grid-like manner from layers dating to the Pleistocene epoch. We retrieved ancient faunal and hominin mitochondrial (mt)DNA from 685 and 175 samples, respectively. The earliest evidence for hominin mtDNA is of Denisovans, and is associated with early Middle Palaeolithic stone tools that were deposited approximately 250,000 to 170,000 years ago; Neanderthal mtDNA first appears towards the end of this period. We detect a turnover in the mtDNA of Denisovans that coincides with changes in the composition of faunal mtDNA, and evidence that Denisovans and Neanderthals occupied the site repeatedly--possibly until, or after, the onset of the Initial Upper Palaeolithic at least 45,000 years ago, when modern human mtDNA is first recorded in the sediments.
A key event in human evolution is the expansion of modern humans of African origin across Eurasia between 60 and 40 thousand years (kyr) before present (bp), replacing all other forms of hominins. ...Owing to the scarcity of human fossils from this period, these ancestors of all present-day non-African modern populations remain largely enigmatic. Here we describe a partial calvaria, recently discovered at Manot Cave (Western Galilee, Israel) and dated to 54.7 ± 5.5 kyr bp (arithmetic mean ± 2 standard deviations) by uranium-thorium dating, that sheds light on this crucial event. The overall shape and discrete morphological features of the Manot 1 calvaria demonstrate that this partial skull is unequivocally modern. It is similar in shape to recent African skulls as well as to European skulls from the Upper Palaeolithic period, but different from most other early anatomically modern humans in the Levant. This suggests that the Manot people could be closely related to the first modern humans who later successfully colonized Europe. Thus, the anatomical features used to support the 'assimilation model' in Europe might not have been inherited from European Neanderthals, but rather from earlier Levantine populations. Moreover, at present, Manot 1 is the only modern human specimen to provide evidence that during the Middle to Upper Palaeolithic interface, both modern humans and Neanderthals contemporaneously inhabited the southern Levant, close in time to the likely interbreeding event with Neanderthals.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, KISLJ, NUK, PILJ, PNG, SAZU, SBMB, SIK, UILJ, UKNU, UL, UM, UPUK
Abstract
Paleogenomic research can elucidate the evolutionary history of human and faunal populations. Although the Levant is a key land-bridge between Africa and Eurasia, thus far, relatively little ...ancient DNA data has been generated from this region, since DNA degrades faster in warm climates. As sediments can be a source of ancient DNA, we analyzed 33 sediment samples from different sedimentological contexts in the Paleolithic layers of Sefunim Cave (Israel). Four contained traces of ancient Cervidae and Hyaenidae mitochondrial DNA. Dating by optical luminescence and radiocarbon indicates that the DNA comes from layers between 30,000 and 70,000 years old, surpassing theoretical expectations regarding the longevity of DNA deposited in such a warm environment. Both identified taxa are present in the zooarchaeological record of the site but have since gone extinct from the region, and a geoarchaeological study suggests little movement of the sediments after their deposition, lending further support to our findings. We provide details on the local conditions in the cave, which we hypothesize were particularly conducive to the long-term preservation of DNA—information that will be pertinent for future endeavors aimed at recovering ancient DNA from the Levant and other similarly challenging contexts.
This cross-sectional study was conducted on the skeletal remains of individuals of known sex, age, and ethnic origin. The vertebral bodies of levels C3–C7 were measured and analyzed. Whereas many ...studies were performed on the size and shape of the vertebral bodies in the thoracic and lumbar spines, few have focused on the cervical vertebral bodies. Thus, there is insufficient data in the literature on the anatomy of the cervical spine, especially based on large study populations.
To establish a large database on cervical vertebral bodies' size and shape and analyze their association with demographic parameters.
The population studied was composed of 277 individuals, adult males and females of African American (AA) and European American (EA) origin. The skeletal remains are housed at the Hamman-Todd Osteological collection (Cleveland Museum of Natural History, Cleveland, OH).
A 3-D digitizer was used to measure the size and shape of the C3–C7 vertebral bodies. Descriptive statistics were carried out for all measurements. t Test and one-way analysis of variance were performed to assess differences in vertebral bodies' size and shape between different demographical groups (by age, sex, and ethnicity).
The vertebral bodies and foramina are significantly wider, more elongated, and higher in males compared to females. AA females and males manifest significantly greater vertebral bodies (width and length) in the upper and midcervical region (vertebrae C3–C5) than EA females and males. Nevertheless, the heights of the C3 and C4 vertebral bodies are significantly smaller among the AA population, regardless of sex. The vertebral foramina's width does not differ significantly between the two ethnic groups, independent of sex, whereas they tend to be elongated in the EA group (significant for C3, C5, C7). For most vertebrae, no significant differences were found in the superior facets' length between AA and EA males and females. Cervical vertebral bodies become wider and more elongated with age, although the changes in the latter dimension are much more pronounced than in the former. Notably, the body shape of the cervical vertebrae changes gradually from a more round shape (C3 length/width index=0.84) to a more oval one (C7 length/width index =0.65). This is due to the fact that the width dimensions increase by almost 40% from C3 to C7, whereas the length dimensions increase only by approximately 10%. Furthermore, there is a significant reduction in body height with age in C3–C6. In contrast, no significant changes in vertebral foramen size with age were found.
The cervical vertebral bodies' shape and size are sex-dependent phenomena, that is, in all parameters studied, the dimensions were greater in males than in females. For the midcervical level, there is a difference in body shape between individuals of different ethnic origins. The cervical vertebral bodies also exhibit considerable size and shape changes with age, that is, they become more elongated (oval shaped), wider, and shorter. In contrast, vertebral foramen size is age independent.
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